Synthesis
by Donaruie
Summary: A possible conclusion to one of the endings if the indoctrination theory is true.


Title: Synthesis

Summery: A possible conclusion for one ending if the Indoctrination theory is true.

Shepard: Male, Paragon, Vanguard, Spacer, War Hero (Blond haired, blue eyed, think stereotypical knight in shining armor)

Author's notes: Jumping on the bandwagon as it were lol. I didn't mind the endings at all but I figure, hey, why not ^.^ I did some actual scientific research into one part on this little dribble. Delicious cyber muffins to anyone who wants to guess which part lol

I based a lot of what happens here on my own play through but I'm sure plenty of it could be easily changed to include other players options and relationships, romantic and otherwise.

Anyway, enjoy!

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><p>Shepard's eyes drifted open. He could feel the smooth surface of the Citadel floor under his cheek where he had fallen. The control panel just within reach if he could get up. Confusion creased his brow. This...wasn't...<p>

The star child...the blue beam...the green wave of energy.

All those things he'd seen. The Galaxy changed forever. United. The Geth. The Quarians. Joker and EDI.

A...dream?

_"Shepard? SHEPARD! Commander do you read me? Please respond!"_ Hackett's voice over the comm was booming, too loud through the silence of the room.

He twitched, tried to respond, but even the tiny movement of opening his mouth seemed too much. Spiking off shoots of stabbing, burning pain throughout his body. He convulsed slightly in response to the torment which only made it worse.

His breath wheezed, forced through bloody lips, as he stared through blurry eyes at the battle still being waged outside.

_"This is The Normandy. Taking a pass by The Citadel to check things out. Damnit...everything's been sealed up. EDI, see what you can do."_

_"Affirmative, hacking systems." _EDI's voice paused, _"I am detecting Shepard's emergency transponder signal. Scanning for life signs. One life sign detected. It is very weak."_

_"Thank God he's still alive." _Hackett said, relief obvious in his voice.

_"He must be out of it, he'd have responded by now...or...fired The Crucible...something."_ Joker, reasonable as always.

_"Neurological scans suggest he is still conscious." _No, EDI...please...I can't do this.

_"Shepard? Come on Son, you've come this far, don't give up on us yet." _Hackett's voice was more subdued, encouraging...begging.

He squeezed his eyes shut, managed to drag one arm up by his head. The effort left him gasping. He activated his comm, taking a few moments of silence as he tried to get his voice to work.

"I...I...can't..." his voice cracked and he coughed, blood splattering the floor.

_"Yes, you can. Think of everything you've done to get this far. Everything you've accomplished. You can do this."_

He grimaced, a sob catching in his throat as he pushed himself to his hands and knees. The pain was everywhere, everything. It was his world. His arms trembled and he started to sink back down.

"...help me...I...can't..."

_"We're doing our best, Commander. EDI's not having much luck. Come on, come on!"_

_"You are not helping, Jeff."_ EDI's voice had an unusual level of strain to it.

_"Stand up, Shepard. You CAN do this. On your feet soldier! It's time we finished this, it's time we were done...Pharos."_

The sound of his name, his first name, opened his eyes. How long had it been since anyone referred to him by his first name? Not even his mother, military officer that she was, called him that anymore.

He grit his teeth and forced himself up with a harsh cry, hands gripping the edges of the console tightly as he leaned against it. He lifted his head and looked out at the Earth...and froze in confusion at what he was seeing.

The planet was awash in a faint greenish glow. The destruction caused by the war erased. Reapers and warships floating by without exchange of fire. Coexisting. So...peaceful...perfect.

_"We've got incoming! Shit, it's Harbinger! Evasive action!"_

_"Shepard! Fire the Crucible! You mu-"_ The transmission fizzled into static.

He swallowed and blinked rapidly as he peered down at the console. The orange glow shimmered and became green.

His dream. It was like his dream. This couldn't be real. What was happening?

There was an ominous buzz and the image of a reaper appeared in front of him. If he hadn't depended on the pedestal to remain upright he would have backed away.

**YOU HAVE SEEN. NOW YOU CAN UNDERSTAND.**

"Understand what exactly?"

**OUR PURPOSE.**

"You told me already. To bring order to chaos by killing organics."

**NO. WE ARE YOUR SALVATION. YOU ARE YOUR OWN DESTRUCTION.**

"I don't understand."

**WE HAVE TRIED TO TELL YOU, BUT YOU DID NOT UNDERSTAND, SO...WE SHOWED YOU.**

"...I don't..."

**SYNTHESIS.**

"...merging of synthetics and organics...all organics..."

**AND THE CYCLE WILL BE ENDED. THERE WILL BE PEACE.**

"But why are you destroying everything?"

**ORGANICS WILL NOT LISTEN. THEY FIGHT. KILL THOSE WHO DO. THOSE WHO RESIST MUST BE HARVESTED.**

"And those who do listen?"

**YOU HAVE SEEN THEM. THOSE WHICH YOU CALL KEEPERS, COLLECTORS, RACHKNI...SAREN.**

"The Illusive Man. Why did you target me?"

**SAREN WAS CHOSEN...BUT HE WAS WEAK...YOU ARE STRONG. YOU CAN LEAD. YOU CAN END THE CYCLE AND BRING PEACE AND OTHERS WILL NOT FIGHT BACK. THEY TRUST YOU.**

"The Collector's killed me on your orders."

**NO. MEANT TO BRING YOU BACK...CERBERUS STOLE YOU FROM US.**

"You mean you meant to harvest me."

**ONLY IF YOU CONTINUED TO RESIST.**

"Of course I would have!"

**YES. WE WERE PREPARED FOR THAT EVENT...BUT YOU DESTROYED THE BODY WE WERE BUILDING FOR YOU.**

Shepard's face twisted in horror as he remembered the Reaper "fetus" they had destroyed.

**IT IS NO LONGER NEEDED. WE HAVE SHOWN YOU WHAT WE WANT AND YOU WERE ACCEPTING OF OUR GIFTS. THE GALAXY WE SHOWED YOU CAN BECOME A REALITY.**

He shakes his head, "You expect me to believe you?"

**IF YOU DO NOT, THE WAR WILL CONTINUE, YOU WILL NOT SURVIVE.**

"We've completed The Crucible."

**IT WILL NOT SAVE YOU.**

"You're wrong." his hands hesitated over the console.

**YOU DO NOT UNDERSTAND. IT WILL DESTROY US...IT WILL ALSO DESTROY YOU. IT IS A WEAPON BUILT BY INSANITY AND DESPERATION. YOU ARE THE FIRST TO COMPLETE IT...BUT YOU MUST NOT USE IT.**

"...You're afraid..."

**YES. IT IS ALL WE HAVE FOUGHT TO PREVENT.**

"Man often finds his fate through the steps he takes to avoid it..."

There is a long pause.

**...THAT IS AN ACCURATE DEPICTION.**

He let his head fall forward and he leaned more heavily against the console.

"...what does it do?"

**IT USES THE MASS RELAY ON THE CITADEL TO SEND OUT A MASSIVE DESTRUCTIVE SHOCK-WAVE ACROSS THE GALAXY DESTROYING IT AND EVERY MASS RELAY IT HITS. YOU KNOW WHAT HAPPENS WHEN A MASS RELAY IS DESTROYED.**

"My god...every system."

**THEY WOULD BE DESTROYED. ALL ORGANIC LIFE BURNED FROM THE FACE OF EVERY PLANET. A GALAXY OF BARREN DESERT WORLDS.**

Fear shot through him. A couple of buttons pressed and they'd destroy everything. His legs shook and he suddenly collapsed to his knees. His breath caught in his throat and he tasted iron. He braced himself as he collapsed into a fit of coughing. He couldn't breath!

**YOU ARE DAMAGED.**

"You...did this...to me." he gasped.

**YOU WOULD NOT LISTEN, WE HAD NO CHOICE. IF WE HAD WISHED TO DESTROY YOU, YOU WOULD BE DEAD. WE CAN HELP YOU, BUT YOU MUST STOP THE CRUCIBLE.**

"I can't...help me first."

There was a loud groaning of metal and the station shook from an impact.

_"*buzz* -pard? Shepard? Can you hear me?"_

"Ash..."

_"Hold on, Skipper, we're almost there!"_

"Ash!...wait...you have to stop it..." his voice cut off as he choked on more blood.

**THEY CAN NOT BE TRUSTED. YOU MUST STOP IT.**

There was an ominous crackle of electricity and Shepard looked up at the Reaper image at the same time it began to glow brighter. Suddenly his entire body became encased in red arches of energy. He stiffened, head thrown back in a scream as the electrical arches flared along his spine, his limbs, flaring in his eyes. His Cerberus implants! Slowly the pain was beginning to fade, strength returning to his body.

Gunshots rang out suddenly, passing harmlessly through Harbringer's image to crack harmlessly into the windows behind it.

"Leave him alone you monster!" Ashley's voice rang out across the room like a siren's call, the reaper's image flickering before fading from existence, his body slumping forward as the last of the energy died away.

"Vega, get the console, get that thing working." she ordered as she hurried to Shepard's side.

"I'm on it!" The marine shouldered his weapon and stepped in front of them, tapping buttons on the console.

Shepard shook his head and then stood up abruptly, faster then he should have been able to in his condition, "No! Get away from the console! Stop!" he shouted, lunging forward and pushing the larger man aside.

"Hey! What's your problem...shit!" Vega exclaimed as fumbled for his weapon.

"Shepard! What are you doing?" Ashley asked, "Vega! Stand down!"

"Look at him!"

Shepard glared at him, he didn't know how he looked. Couldn't see the split scars on his face or the exposed ocular implants. As he placed his hands on the console though he could see the mechanical blue glow of tech beneath the blood. It made him pause, but he couldn't stop. His hands flew across the console. There was a slight jolt and the station suddenly began to pull back, the arms closing.

_"Hackett here. What the hell is going on?"_

Ashley's eyes were wide and she turned away from the console, "It's Shepard, Sir...I think...I think he's been indoctrinated..." her voice was somewhat unsteady. The silence was a long one and she heard a soft click in her ear and she raised her fingers to it.

_"I'm switching to a private channel. If what you say is true, you know what you have to do."_

"Sir, I..."

_"I know how hard this must be for you. I don't care how you do it, but those arms MUST be opened. We don't have the time. Do what needs to be done."_

"I...yes...Sir." she steeled herself as she turned around, drawing her gun only to freeze as she found herself already staring down the barrel of Shepard's pistol.

Mechanical eyes narrowed, "Don't. Please...Ash, I don't want to hurt you."

Her own eyes narrowed, matching his determination with her own as she defiantly raised her own weapon, "Put the gun down, Commander. You don't want to do this."

"I can't let you fire The Crucible. You have to trust me, Ash...if ever there was a time you trusted my judgment or cared about me at all, trust me now!"

She shook her head, "You're indoctrinated!"

"No, it's not like that! The Crucible will destroy everything! I can't let you use it! I'm not their pawn, I was dying, they helped me to keep you from making a mistake!"

"Would you kill me for not believing you?"

His gun hand trembled and his stern facade faltered, "This is bigger then you and me, Ash...please, trust me."

She blinked and held her hands out, gun pointed away, "I do trust you Shepard..." her eyes flicked to something behind him, "...it's them I don't trust."

Suddenly he was grabbed from behind, muscular arms gripping him beneath his arm pits, pulling his back and causing him to drop his gun, "Sorry, Jefe." Vega's voice grunted, "But you're not in the best condition to be givin orders."

Shepard growled and stepped back into the larger man, slipping one foot between Vega's and throwing his head back into the other man's nose. The marine staggered and tried to keep his grip but was tripped up by Shepard's foot, forced to let go to catch himself.

Turning to face the Marine he sneered, "Didn't your old CO ever tell you, James? Muscle doesn't mean anything if you don't know how to use it." Shepard's body began to glow blue with biotics, "Even less when dealing with a biotic." he threw one hand out and threw the man against the far wall. Shepard crouched and Ashley saw the tell tale way the blue energy formed in front of him that indicated he was going to Charge.

"James!" she tried to call out a warning but it was too late, the vandguard already in motion, going from perfectly still to the other side of the room in the blink of an eye, plowing through the marines kinetic barrier and sending him back into the wall with bone shattering force. It was hard to tell if the snapping sound had been his armor or something more lethal as he slumped to the floor in a rag-doll manner she recognized all too well.

Muttering a curse Ashley turned to the console and her fingers flew across the panel, the station shuddering as the arms once again began to open.

"No!" Shepard cried running back towards her, stopping as Ashley spun and trained her gun on him.

He held his hands up, his expression pleading, "You can't use it!"

"Watch me!"

"It'll detonate the Mass Relays!" he yelled as she started to activate the docked Crucible, she froze, eyes wide.

"It...are you sure? Who told you that? Them? And you trust _them_?"

"I can't take the chance...and neither can you."

She looked back and forth between them, pulling her hand back from the panel, "Shit..."

"We don't have to fight them. I wish I could show you what they showed me. You'd understand then."

The grip on her gun tightened and she gave him a hurt look, "I will never trust them, nothing you say will ever make me trust them. They're not doing a very good job of showing how benevolent they are. You say we don't have to fight? Prove it...or I'm taking our chances with the Crucible. Trust goes both ways Pharos, you want me to trust you? You have to trust me too. They're lying to you. They've made you kill for them! This isn't you!"

He took a long moment to consider it. His mind kept going in circles. That he trusted them and so she should trust him, anything else was betrayal. betrayal meant death...to everyone. He had to kill anyone who got in his way. Anyone. His brow furrowed and he shook his head forcing his mind past the notion. She would never willingly betray him. If that were true, and he knew it was, then she was just trying to help. Even if it was misguided in his mind.

"Harbinger?"

The image of the reaper reappeared.

"Trust goes both ways. If you want us to trust you, you must trust us."

**EXPLAIN.**

"Pull your forces back. From every planet. Stop attacking us."

There was a long moment of silence.

**UNACCEPTABLE. THE CRUCIBLE MUST BE DESTROYED.**

"If you do as we ask, we will destroy it ourselves."

**UNACCEPTABLE. ORGANICS CAN NOT BE TRUSTED. CLOSE THE CITADEL AND ORDER YOUR FORCES AWAY.**

Shepard's eyes narrowed and he glared at the image, "No."

**WE GAVE YOU A CHANCE. YOU HAVE FAILED. ASSUMING CONTROL.**

The reaper image disappeared and Shepard cried out, his body wreathed in energy, staggering as he fought the sudden invasion to mind and body.

"Shepard!" Ashley cried as the body of her Commander, her lover, turned to face her. There was almost nothing left of the man she had known, the flesh all but melted away around a skeleton of glowing metal and arcing electricity housed in ruined N7 armor.

"No..." she whimpered even as she lifted her weapon and opened fire. An aura of blue mixed with the red as the commander's usurped biotics mixed with the reaper tech to form a kinetic barrier, absorbing the damage. It reminded her of the banshees. She grimaced and backpedaled away from the advancing thing even as tears trailed down her cheeks, continuing to unleash a barrage of thermal clips. One of the clips punched through the barrier and buried into his shoulder but it only seemed to anger him and she was met with a biotic shock-wave that threw her back and off her feet. Just as suddenly as she hit the ground he was suddenly on top of her, the sparks flying around her, stinging her skin. She cried out as the claw like hands tried to claw at her throat and face.

"JOKER! DO IT!"

The thing that had been Shepard turned it's head, seeing The Normandy just outside the window.

_"I...I can't do it again...it's Shepard...there's gotta be a way to save him!"_

Shepard suddenly shuddered and cried out, pulling away from her and gripping his head. A voice sounded through the comm.

_"EDI...you know...what to do."_

_"Yes, Commander. Powering weapons." _EDI's voice was calm but there was an undertone that they had never heard from her.

_"EDI...no...what are you doing?"_

_"I am sorry, Jeff. Better to be dead then serve the Reapers. Goodbye...Pharos."_

Even as the ship opened fire Shepard let out a mechanical shriek and lurched toward Ashley. Their was a faint hissing sound and then the windows exploded outward into the vacuum of space. Ashley screamed as she began to fly out, the air forcefully expelled from her lungs like a kick to the stomach as the pressure plummeted, only to jerk to a halt, a mechanical hand gripping her shoulder even as the opposite hand anchored the husk in place.

No, she realized as she stared at him, seeing something familiar in the way it was looking at her. Shepard was still there. The air was gone from the room and she could feel consciousness leaving her.

Shepard gazed out at the stars beyond the shattered windows. The silence of the vacuum that filled the room. It pulled at him, a part of him that the Reapers would never be able to understand. The same feeling that he had felt ever since Cerberus had brought him back. That he belonged out there. That he had never been meant to return. An almost spiritual longing he would never have been able to express to his friends without seeming suicidally unstable.

It gave him the control he needed, leaving Ashley to float where he had held her. He had to hurry if she were to survive. Two minutes. Two minutes his mother had always drilled into his brain. You could survive that long in vacuum and still be able to recover. He clawed his way towards the console, fighting the Reaper's for every inch.

**YOU CANNOT RESIST US.**

Harbinger's voice shouted in his mind as he pulled himself up to the console.

"Watch...me..." he growled back as he punched in the sequence ignoring the Reaper's deafening shrieks of anger.

"It's...over." he sighed as the Crucible began to activate and the blast shields for the room slid into place, a loud hissing as it pressurized. Crawling back over to Ashley he held her as she gasped and coughed, blood leaking from her eyes and nose, her face swollen. It was normal, she'd be fine. She blinked up at him and he put a hand to her face as the room began to shake. The Crucible was firing.

"Forgive me. I love you."

"Shep..." she started but didn't get a chance to finish as a wave of energy plowed through the room, leaving crackling arcs of energy along every surface. The lights dimmed and went out and Shepard collapsed, the glowing implants on his body flickering briefly before fading away.

Ashley gasped and then began to sob, left in the dark. She pressed her fingers against her ear trying to activate her comm.

"Hello? Is anyone reading this?" nothing...not even static. "Hello?" she whispered brokenly a couple more times before finally giving up and completely submitting to her grief.

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><p>-12 hours later-<p>

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><p>Ashley didn't know how long it had been, not even the clock on her suite worked, that she'd been sitting alone in the darkness. Waiting. She was dozing lightly when something abruptly woke her up. A hum. What was that? A second later the overhead lights flickered and blazed to life, making her cover her eyes in discomfort.<p>

_"Hello? Anyone reading this?" _An unfamiliar voice sounded over the comm.

_"This is *static*-for-*static* operating base. *static*Who is that?"_

_"This is C-sec security. Had to do some hard resets on a lot of the operating systems. Everything got knocked out. What's your situation?"_

_"The same down here. Everything electronic was knocked off line."_

_"The Reapers?"_

_"Everything electronic."_

_"My god! How?"_

_"Info is a little sparse down here, but all bets are on The Crucible. Williams must have fired it. Some sort of huge EMP wave, it's gonna be a while before we get everything back up and running."_

Ashley squeezed her eyes shut as she looked down at the ruined body of her lover, she slowly activated her comm.

"It wasn't me."

_"Williams? That you? You alive up there? Hold on, we'll get you out!"_

She shook her head, "It wasn't me...it was Shepard. He saved us all."

She didn't hear the rest of the conversation as she hugged the body closer to her, "You hear me? You're a Hero...there's nothing to forgive. Nothing. You sleep now. You've earned the rest, skipper."

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><p>-Fin-<p> 


End file.
